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Gaius Baltar is from the colony of Aerelon, a largely agricultural world that was known as the "food basket for the twelve worlds". He was born and raised on a dairy farm outside of the town of Cuffle's Breath Wash. At the age of ten, finding the Aerelon dialect (demonstrated by James Callis as represented with a coarse Yorkshire accent) to be detrimental to his career dreams, he trained himself to speak with a Caprican dialect (represented by refined English, specifically Callis' usual Received Pronunciation) in hopes that one day he might be considered a citizen of one of the more respected and wealthy colonies, Caprica in particular. His father scorned him for despising his Aerelon heritage, and performing what he described as “an honest day's work” on the family farm. This implies that a number of colonies (for example Sagittaron and Gemenon) are not only poor worlds, but also viewed as intellectual and cultural backwaters. According to his account, Baltar left Aerelon after his 18th birthday.

Baltar eventually became a brilliant computer scientist and an important defense researcher on Caprica, and a personal friend to President Richard Adar. He was perhaps best known for his controversial views on research into Strong AI, saying in an interview: "The ban on research and development into artificial intelligence is, as we all know, a hold-over from the Cylon Wars. Quite frankly, I find this to be an outmoded concept; it serves no useful purpose except to impede our efforts."

At the onset of the miniseries, he is involved in an intense sexual relationship with a beautiful blonde woman. Believing her to be working for a corporation in the defense industry, and desiring a more permanent relationship with her, he gives her access to the Colonial defense mainframe so her employers can have an advantage in future contract bidding. In exchange for his access to government mainframes she helps him design a navigation program used by Colonial warships, covertly creating backdoors in the program. When the Cylons attack, they are able to penetrate software security firewalls, disabling entire fighter squadrons outright and sabotaging vital capital-ship systems. On the day the Cylons attack humanity, she reveals that she is an advanced Cylon (known as Number Six) and that she used the information given to her to shut down the Colonial defenses.

Having unintentionally brought about the near-annihilation of the human species, Baltar flees Caprica when Karl Agathon gives up his place on a Raptor, feeling that his own life is less important to save than a famed scientist's. The Raptor returns to the Battlestar Galactica, where Baltar endears himself to Laura Roslin, the new President of the remnants of the Twelve Colonies, and hopes to conceal his involvement in the genocide that has taken place.

Once a part of the fleet, Baltar is haunted by visions of Number Six, with whom he converses often. It is unknown whether these projections are from a chip that Number Six implanted in Baltar's brain while they were together on Caprica (the explanation originally given by the Number Six vision, which she later disclaimed) or if she is simply a manifestation of Baltar's own mind. Although the vision of Number Six manipulates Baltar through his fear of discovery, she lends him an edge by granting him unique knowledge and helps him overcome weaknesses in his personality.

The model of Number Six who had seduced him on Caprica later experiences similar visions after her consciousness was downloaded into a new body. Whereas Baltar experienced visions of her, she experienced visions of him. Both visions acted in similar ways: they were seemingly crueler than the person they were based on and often manipulated the affected party against his or her own species.

Shortly after Baltar comes on board Galactica, his Internal Six reveals that a device has been put in the CIC that he had previously seen in possession of Six on Caprica. Six tells him that it wasn't her job to put it in the CIC. Baltar realizes that there is a Cylon on board Galactica, but knows he cannot reveal that information, or indicate that the device is not a part of the ship without implicating himself in the destruction of the Colonies. Baltar decides to implicate a person on board who goes by Aaron Doral because he is a civilian who has had access to the CIC during the last several weeks and, as an outsider, would be more likely to be untrusted by the Galactica crew. Having already been put in charge of testing the fleet for Cylons, Baltar informs the Executive Officer that he discreetly collected hair samples of crew members and has found that Doral is a Cylon. Baltar, however, had no method at the time for testing for Cylons in the fleet. Baltar also explains that he saw Doral doing something with a strange looking device in the CIC that he does not recognize. With this (Doral is, it turns out, indeed a Cylon), Baltar is able to protect not only the fleet, but his own interests as well.

Unfortunately for Baltar, this forces him to develop an actual method for testing the fleet for Cylons, having already 'demonstrated' an ability to do so. The process he eventually creates is reliable and is done through the testing of blood samples, but is time consuming (it takes 11 hours to test one person). This meant that it would take 61 years to test the entire fleet, and makes Baltar feel his work is of little importance.

In the episode "Six Degrees of Separation", Baltar is accused of being a traitor to the human race when a flesh-and-blood Number Six (after Baltar and his Internal Six have a heated argument over whether or not God exists) shows photographic evidence that Baltar carried an explosive device into the Colonial Defense Mainframe on Caprica, allowing the Cylons to carry out their nuclear attack. When it is found that the evidence is faked, President Roslin holds a press conference publicly exonerating Baltar. Internal Six tells him that his public position is now stronger than ever since he has been accused of a serious crime and found innocent, and even possibly been the target of a Cylon plot. Meanwhile, the real-life Six disappears from Galactica and is nowhere to be found.

In the episode "The Hand of God", Baltar successfully helps the fleet destroy a Cylon mining base on an asteroid with badly needed tylium ores for fueling the fleet. Because the base could not be nuked (as the radiation would render the ores inert), the best plan for the attack was to destroy the part of the base holding the volatile unrefined tylium precursor (in order to create a large explosion). The planners of the attack ask Baltar to point out where it is on a recon photo, even though he has no idea what it looks like. In his mind, Baltar asks his Internal Six for help, but she tells him it is in God's hands and He will 'tell' Baltar where to point. Baltar then points to one of the buildings of the base, simply as a wild guess (although he doesn't tell the others that). Baltar is terrified, telling Six he didn't hear God's voice, but she reassures him: "God doesn't always speak in words." Much to Baltar's surprise, his wild guess at which building held the volatile tylium precursor was correct. Baltar then realizes that the only logical explanation could well be that God truly did guide his hand.

In the episode "Colonial Day", Baltar demonstrates surprising charisma when he attacks vice presidential-hopeful Tom Zarek on behalf of the President while being interviewed by the fleet's media. This, coupled with Baltar's newfound fame from being falsely accused of treason, convinces Roslin to choose Baltar as her vice president over a previous choice. In the end, Baltar defeats Zarek in their race for the Vice Presidency.

In the second season episode "Home, Part II", Baltar undergoes a brain scan similar to an MRI which reveals no sign of a computer chip or any other foreign object in his brain. While this briefly leads him to think that he had truly gone insane, he then realizes that the vision of Number Six he sees could not possibly be a hallucination generated by his subconscious mind, because she is aware of facts that his own mind could not possibly know. Number Six tells him that the first Human/Cylon Hybrid will be born in the ship's brig, and soon after the Caprican version of the Cylon Sharon Valerii (pregnant with the human Karl Agathon's child) is imprisoned in it. When Baltar confronts Six with this, she states that she was neither a computer chip nor a hallucination. When Baltar then asks just who or what she is, she simply replies that she is "an angel of God sent here to protect you, to guide you, and to love you".

Baltar's relationship with Six was further complicated by the appearance of Gina, another Six copy who had been posing as a maintenance worker on the Battlestar Pegasus. After discovering Gina, who had been repeatedly tortured and raped by Pegasus crewmembers, Baltar grows fond of her, making the illusory Six jealous. He eventually helps Gina escape from the Pegasus and arranges a place for her safety. Gina later forms a pacifist movement within the fleet, although it is noteworthy their methods are not always peaceful, and Baltar is initially reluctant to support the organization despite his affections for her. Later, however, after saving President Roslin from terminal cancer, he reads the letter she had left for him to be opened upon her death (a custom performed by all presidents, written to their successors upon their leaving office) which states he has a "selfish nature" and asks that he overcome it for the well-being of the fleet. Afterwards, Baltar's vision of Number Six persuades him to give Gina and the movement a nuclear bomb Admiral William Adama afforded him in an earlier episode to test the fleet for Cylons.

Having been offended by Roslin's letter, and encouraged by outspoken Roslin-critic (and Baltar's former opponent in the race for Vice President) Tom Zarek, Baltar announces his intention to run against incumbent Laura Roslin for the presidency with the next election approaching. He does this by surprising both her and the press at a press conference after Roslin's announcement of a moratorium on abortion. Baltar hijacks the conference, establishing himself as a candidate and secular alternative to the molded prophet-like image of Roslin.

Baltar, with Zarek as his close political advisor, proceeds to run a bitterly contentious campaign against Roslin. He is far behind Roslin in the polls during most of the election and is able to make limited progress only by painting her as a dangerous religious fundamentalist. With little time remaining before the election, a desolate but habitable planet is accidentally discovered in a region of space where heavy electromagnetic interference makes navigation and long-range observation very difficult. Baltar, although he has no personal desire to settle on the planet, announces that he will begin immediate civilian settlement of "New Caprica" if elected. With Roslin opposed to settlement on the planet, Baltar's popularity quickly rises. Fearing that she will lose the presidential race, Roslin holds a private meeting with Baltar, asking to deliver a joint statement of tabling the issue of colonization until after the election (which he rejects). Roslin then confronts Baltar on whether he was with a copy of Number Six on Caprica before the Cylon attack (At the height of her illness from cancer, Roslin had a flashback of an encounter between Baltar and Number Six prior to the Cylon attack, but was not able to fully process her memories at the time). Baltar avoids answering the question and leaves.

Due to his support for settlement of New Caprica, the election promptly swings in Baltar's favor and, after an attempted conspiracy to commit voting fraud fails to keep Roslin in power (organized by Roslin herself), he wins a narrow victory and is sworn in as president. Just prior to his inauguration, Baltar visits Gina, who makes love to him for the first time (she had previously refused physical intimacy, having suffered severe emotional and physical scarring from being repeatedly raped aboard the Pegasus). During the inauguration itself, she detonates the nuclear warhead that Baltar had given her, destroying the luxury liner Cloud 9 and killing herself in the process. Following this apparent act of Cylon nuclear terrorism, Admiral Adama urges Baltar to immediately focus on internal security and investigate how a Cylon agent could have carried out the bombing. Baltar refuses, however, and stubbornly proceeds with plans for settlement.

Baltar remains in office for one year, but his feelings of guilt (or possibly just his fear of being discovered) regarding his involvement in both the fall of the colonies and Gina's suicide bombing, combined with the stress of the presidency and his inexperience in dealing with policy matters, have led him to substance abuse and womanizing, which he does not hide from his Chief of Staff Felix Gaeta. Life on New Caprica has turned out to be extremely difficult, with the civilian population living in extremely rough conditions, and with shortages of basic supplies like antibiotics persisting. In addition, Baltar's government is in the midst of a major labor dispute with a union led by Galen Tyrol, who is advocating a strike for workers' rights. Baltar indicates to Gaeta that he may be willing to jail union organizers if the labor disputes continue.

The political difficulties faced by Baltar's administration are soon made irrelevant, however, when a Cylon fleet arrives in orbit of New Caprica. The remaining military fleet, which has been operating using skeleton crews, jumps away, leaving New Caprica to be occupied by the Cylons. A Cylon delegation, which includes the reborn versions of both the Number Six who had originally seduced Baltar (now known by the other Cylons as Caprica-Six) and the Sharon Valerii who was originally stationed on Galactica, lands in the human settlement and accepts Baltar's surrender. When Baltar asks how the Cylons managed to detect New Caprica, it is revealed that they were a light-year away when they detected the light and radiation from the nuclear explosion Gina set off the year before. Baltar has thus once again inadvertently aided the Cylons in their subjugation of humanity.

Baltar continues to hold the office of the Presidency, but only as a figurehead. 133 days after the Cylons land on New Caprica, a Doral model Cylon states that most humans have come to consider Baltar a traitor and would rejoice in his death. Compounding his alienation to his people, he was forced at gunpoint to sign an execution order for hundreds of humans. However, throughout the occupation of New Caprica, Baltar tried to persuade the Cylons that their mission to rule over the human race could not succeed and that they should leave the planet. Before he evacuates the planet with Caprica-Six, Baltar reveals he has been having suicidal thoughts.

As the Colonials evacuate New Caprica, Baltar and Caprica-Six discover Hera, the child of Sharon "Athena" Agathon whom Six predicted would be born in Galactica's Brig. Roslin, it turns out, had hidden Hera's existence by falsifying her death and secretly allowing a young mother to adopt the child as her own.

In the episode "Collaborators", we find Baltar living on a Cylon Basestar in a barless cell furnished with only a bed, a table, and a bathrobe, guarded by a Centurion. It is here that Caprica-Six tells Baltar that she has had a change of heart about him and has let her feelings for him cloud her judgment, presumably ending their relationship. However, by the end of the episode, it is indicated that she has cast the tie-breaking vote amongst the Cylons to allow Baltar to remain alive aboard the Cylon Basestar, although it is clear they remain estranged.

Over time, Baltar becomes accustomed to his new environment. Once Baltar learns that no one knows what the "Final Five" Cylons look like, he begins to suspect that he himself may be a Cylon. He admits however that this is wishful thinking on his part, because of his desire to have all his 'sins' forgiven and become a hero to another people, rather than be a scourge to his own.

Shortly after he begins living with the Cylons, Baltar is allowed to investigate a stricken Basestar that had fallen afoul of a disease because of his supposed immunity. Baltar is adamant about doing this because he is desperate to prove his loyalty to the Cylons and avoid death, although he requires convincing from his internal version of Six. Once Baltar is on board the Basestar, he finds the origin of the disease—an ancient human probe. Baltar chooses not to tell the Cylons about the probe, in fear that it will implicate him in the spreading of the disease (the Basestar went to its location only because Baltar directed it there to aid the Cylons in their search for Earth). Once the probe is discovered by the Cylons, Baltar is tortured by a highly suspicious Three model known as D'Anna Biers, who uses a set of metal leads covering two fingers on his left hand, creating intense pain with no actual physical damage. During his torture, Baltar is able to induce some form of spiritual epiphany in D'Anna with the help of his Internal Six, and is let go after apparently declaring his love for D'Anna while staring at his vision of Six. He subsequently had repeated ménage à trois with both D'Anna and Caprica-Six (indicating she and Baltar re-formed their relationship).

Towards the end of Baltar's stay with the Cylons, he grows much closer to D'Anna, who has become obsessed with finding the identities of the "Final Five" Cylons. Pondering if he himself is a Cylon, Baltar brushes Caprica-Six aside and aligns with D'Anna. Together, in the episodes "Eye of Jupiter" and "Rapture", Baltar and the Three models defy the other Cylon models and he and D'Anna travel to the surface of an algae planet in search for an ancient ruined temple. Three believed the temple would show her the identities of the Final Five. D'Anna appears to see the Final Five, but collapses and swiftly dies before she can tell Baltar whether or not he is a Cylon. She does, however, say "You were right", possibly indicating that Baltar is in fact a Cylon, although it is unclear to what she was referring. Hoping to retrigger the vision, Baltar steps onto the platform that D'Anna used, when Chief Tyrol gets the drop on Baltar and knocks him out. The ex-president is then transported back to Galactica in a body bag and sent to the brig. Baltar and Caprica-Six re-establish their relationship later in the series because she took refuge with the Colonial Fleet after helping Sharon "Athena" Agathon retrieve her child, although the two are unable to meet in person as she is imprisoned on Galactica.

Following a failed suicide attempt in his cell, Baltar is threatened with death from President Roslin (although she is actually bluffing). Roslin orders Colonel Tigh to throw Baltar out of one of Galactica's airlocks, while repeatedly demanding whether he even knew any of the people who died during his presidency. After pointing out a man along the Galactica's memorial wall (a former lab aide of Baltar's) and reciting almost encyclopedic knowledge of the man, Roslin allows Baltar to be returned to his cell. He is then subjected to a radical form of hallucinogen-based interrogation by Admiral Adama, who convinces Baltar that he is drowning, and that Adama will only save him in return for information. However, Baltar does not have much useful information for Adama. In the course of his interrogation, Baltar admits his unwitting complicity in the original Cylon attack on the Colonies, although without any specifics. Because his admission was extracted through illegal proceedings, this information could not be submitted at a trial. Felix Gaeta is then drafted to offer Baltar the possibility of escaping execution and getting better treatment in exchange for cooperation, as Adama, Tigh and Roslin seek to learn any clues to Earth's location that the Cylons may have obtained from the Temple. Baltar reveals that he has some hold over Felix Gaeta, as he assures Gaeta that his personal demons will be "our little secret" (it is unknown what Baltar was referring to, if anything), shortly before Gaeta stabs Baltar in the neck with a fountain pen (narrowly missing the carotid artery, which would have killed Baltar). Throughout these events, Baltar repeatedly demands a fair trial. Roslin finally decides to reject Adama's suggestion that Baltar be made to "simply disappear" and orders him to be given a trial for his crimes, even after a warning from Tom Zarek (now Vice President) that doing so will provoke dangerous unrest among the fleet's civilian and military populations alike.

Meanwhile, Baltar smuggles writings out of his cell through his lawyer, which are published in a memoir, My Triumphs, My Mistakes. In the book, Baltar attempts to explain his actions as President to the public and foment class warfare by describing the fleet as a bifurcated society, accusing the elite upper class of militarism and professional civilians of exploiting the less well-educated working class. While the book is not completed at the end of Season 3 (President Roslin confiscates several sections through repeated searches of Baltar's cell), it becomes very popular among certain segments of the fleet populace (despite Roslin's repeated attempts to suppress its distribution), including workers on the tylium refinery ship and Chief Tyrol's flight-deck maintenance crew, as well as his wife Cally Tyrol. The book's popularity leads to Tyrol calling a general strike and exacerbates the fleet's already strained social order. This development is ironic due to the labor difficulties Baltar experienced with Tyrol on New Caprica.

As his trial proceeds, Baltar's first lawyer is killed in an explosion aboard a sabotaged Raptor. His second attorney, Romo Lampkin, survives a similar attempt on his life. Lee Adama (now Lampkin's security adjutant) then joins Baltar's defense team. Following Lampkin's questioning of Saul Tigh, Lee has a falling out with father and resigns his military commission.

The trial is unfair, and includes witness Felix Gaeta deliberately lying to ensure a guilty verdict (though Felix may have done so to see Baltar dead before his secret could be revealed). Throughout the trial, the defense deals devastating blows to the prosecution's witnesses, but this only further exacerbates the existing hatred of Baltar in the courtroom. Baltar rejects his defense team's suggestion to demand a mistrial saying, "there will be a verdict." Later, in the days preceding the conclusion of his trial, Baltar is informed by Caprica-Six via Lampkin that President Roslin has discussed her chamalla-induced religious visions with her and Athena.

The defense team uses the very end of the trial to try and persuade the jury (with a passionate testimony of Lee Adama) that Baltar is guilty merely of being a scapegoat for the Cylon occupation. In other words, whatever mistakes he had made as President, he is not guilty of treason. Lee Adama also mentions that the fleet has forgiven numerous other persons for their mistakes because they have had to in order to ensure their survival, and that Baltar is on trial only because he has become a symbol of the pain and guilt that many still feel about what happened on New Caprica. The argument is successful and Baltar is found not guilty for his crimes by a 3-2 vote, with Admiral Adama casting a vote in Baltar's favor. Roslin is disgusted that Baltar is now free as she still truly believes that Baltar was involved in sabotaging the colonial defenses in the attack. After Baltar is freed from prison, his defense team abandons him. Baltar realizes that despite his victories, he has neither a home nor any friends, and is alone among a fleet that overwhelmingly hates him.

Fortunately for Baltar, shortly before the Cylon fleet attacks at the Ionian Nebula, Baltar is led away to safety by three female followers of his work, one of whom had asked him to bless her sick child before his trial. He is received warmly by a group (with mostly female members) that has erected a shrine to him in an unused compartment of Galactica. Baltar quickly learns that he has no other place to go, and must stay on the ship. As the others leave, one of the young women stays behind with Baltar; she is fascinated by the way he appears to be praying with his hands clasped (although Baltar is really responding to his Internal Six). The woman tells Baltar that she feels her prayers to the Lords of Kobol have not been heard. At the suggestion of Six, Baltar convinces the woman that there is only one God. The young woman is overjoyed to hear this and the two make love. Shortly afterwards, the woman who came to Baltar in his prison cell earlier, returns from the infirmary with her son who is very sick and near death. Once the cult members go to sleep Baltar prays softly to God to spare the child's life and take his instead. However, the child's mother and a few other women are still awake and overhear the prayer.

While in a public restroom (Baltar wanted a shave), he and another woman from the cult are later ambushed by two men, one of whom is Charlie Connor (featured in the episode "Collaborators" as the member of The Circle who pushes the button that executes Jammer), who noticed Baltar being led to his new home earlier in the episode. Connor blames Baltar for his own son's death on New Caprica. As he holds a razor to Baltar's throat, Internal Six asks him if he was serious about dying to save the sick child. Baltar reiterates his desire to die in the sick child's place. Connor is suddenly stunned and the woman from the cult then overcomes and incapacitates (probably killing) both assailants. Afterwards, she claims God gave her the strength she needed. Upon returning to the sick child, Baltar finds he has been miraculously cured, with no trace of a fever.

Shortly thereafter, Tory Foster (President Roslin's chief aide) is sent by the other revealed "Final Five" Cylons to seduce Baltar and learn if he knows the identity of the last of the Final Five. While eating in a mess hall on Galactica (with the door being guarded by two male followers of the new Monotheism religion), Baltar sees Foster is present and easily deduces that she is spying on him (believing she is doing so on orders from Laura Roslin). While the two begin to converse, Baltar sees a vision of himself (probably the same vision that Caprica-Six sees). At first, Baltar is shocked, but his Internal Self tells him to focus on Foster because she may be a good source of information. Foster tells Baltar she believes he is the center of recent miracles (the healed child and the fact that Kara Thrace returned shortly after the conclusion of his trial). Baltar says God must have chosen him to "sing his song." Because Foster and the other Final Five became aware that they were Cylons through a mysterious song, she is dumbfounded by Baltar's eerily similar description of how God's plan is like an orchestra tuning up until their notes "slide into place." As a result, she becomes anxious and promptly leaves. Baltar then begins to question his Internal Self as to his identity. The Virtual Baltar tells the real Baltar that he is not Internal Six and then changes the subject to Foster. The two agree that Baltar should see her again. Later, Foster and Baltar have sex. Afterward, Tory says she could be a Cylon, but Baltar tells her not to be afraid and that he has learned from his time among them that Cylons have feelings. He says that humans may have made the Cylons, but it was the one true God that gave them souls.

After his following on Galactica is attacked by a polytheist group, Baltar (with the encouragement of his Internal Six) disrupts a religious ceremony of one of the polytheist denominations in the fleet. Later, President Roslin meets with the imprisoned Baltar to pressure him to avoid stirring up more trouble in the future. After he is released, Baltar is prevented from returning to his home by government soldiers acting under new legislation approved by the President. The legislation restricts the right to assembly specifically for Baltar's movement. Under the direction of Internal Six, Baltar keeps attempting to re-enter his home, and is subjected to repeated blows from a Galactica marine. Internal Six is shown physically lifting Baltar from the floor to a standing position; whereby camera pans across a couple views to allude to Baltar's view of the action and then the view of this action in the context of everyone else present. While we see Baltar's perspective, everyone else only sees a limp Baltar rising to a vertical posture. Their facial expressions appear to allude some sort of supernatural experience is occurring. This event continues until Lee Adama arrives to inform Baltar that the Quorum of Twelve has overruled the President and revoked the new legislation. Baltar goes on to preach that God loves all humans regardless of their sin because everyone is perfect just as they are. Foster is present at the speech and now appears to be a firm supporter of Baltar and his religion.

Baltar's religious speeches are eventually illegally broadcasted to the fleet and his following gradually grows larger and larger. Baltar's sermons include the importance of forgiveness and looking towards the future instead of the past. On Galactica, Tyrol attends another sermon by Baltar. When Tyrol tries to leave just as the sermon begins, Baltar calls on Tyrol to stay. Baltar tells Tyrol that he knows they've had differences, but that he should come and take his hand. When Tyrol does not respond, Baltar then says tells him that Cally (Tyrol's recently deceased wife) would have wanted him to take his hand. Tyrol decides to choke Baltar and furiously shouts that Baltar knew nothing about Cally just as Baltar's followers force him to leave. Later, against the warnings of his followers, Baltar pays a visit to Tyrol's quarters. Tyrol is present and Baltar nervously apologizes for his presumption about Cally and admits that he barely knew her. Baltar then attempts to commiserate with Tyrol about how hard it is to "make sense of things sometimes", but says that he knows there is a purpose to everything that happens. Baltar then admits to having done heinous crimes in the past and says he feels his sermons are his last chance at redemption (in order to provide context for why he got carried away earlier). Finally, Baltar says he is truly sorry for Tyrol's loss and that he wished he had known her better. As Baltar starts to leave, Tyrol holds out his hand in friendship and Baltar eagerly accepts it.

Shortly thereafter, Kara Thrace informs the once again cancer-stricken President Roslin that the Cylon Hybrid on the captured rebel Cylon Basestar referred to a "dying leader" learning the "truth of the opera house"—the setting of the dreams Roslin shares with Caprica-Six and Athena. As Baltar's popularity continued to increase, he choose to inform the fleet of Roslin sharing her visions with both of the long-time Cylons in the fleet. Although this development distressed Roslin, she decides to bring Baltar with her (along with Karl Agathon—Athena's husband) to the Cylon Basestar to see the Hybrid. She informs Baltar that she chose to do this because she sees him in the dreams she shares with Caprica-Six and Athena. The Basestar jumps away from the fleet the moment the Hybrid is reactivated to begin a series of jumps to reach the Cylon Resurrection Hub, leaving Baltar once again away from the fleet aboard a Cylon ship. When the Basestar jumps away from the Colonial Fleet, Roslin begins to have a series of visions involving Elosha, a deceased priestess. The visions continue to develop with each jump.

Baltar and Roslin attempt to interrogate the Hybrid, provoking it to yield cryptic fragments of information. Later, during an attack on the Cylon Resurrection Hub, Baltar initiates an intriguing dialogue with his Centurion guard. Baltar attempts to proselytize his monotheistic ideas, and while the Centurion's reactions are open to interpretation, it appears that some impact is made. However, the Centurion is destroyed while partially shielding Baltar from an explosion that injures him severely.

Baltar is then taken under the care of Roslin. After he is influenced by morpha administered by Roslin, Baltar reveals the details of his involvement in the attack on the Colonies. Roslin decides to kill Baltar by leaving no pressure on his wounds. Baltar pleads to Roslin not to kill him, but he is ignored. At that moment, the Basestar jumps again and Roslin's continuing vision of Elosha on Galactica culminates in an extended discourse on the need to respect the rights of the living, even the despised. Afterwards, Roslin panics and tries desperately to save Baltar's life, acting as if he were a close friend. Baltar recovers and is then reunited with the freed D'Anna. Later, Baltar thanks Roslin for choosing not to murder him.

When the Basestar arrives at the Colonial Fleet, D'Anna assumes command and holds all Humans on board hostage. Roslin decides to try to convince D'Anna to stand down, but allows Baltar to go instead at his suggestion. Baltar convinces D'Anna to abandon another failed attempt at 'brute force' (referring to the events on New Caprica and the Algae Planet) and she cooperates with Interim-President Lee Adama. With the route to Earth now revealed by four of the Final Five Cylons via Kara Thrace's Viper, the combined fleet of Humans and Cylons arrives at Earth (with Baltar among the first to land on the planet). He and others are shocked to find Earth is a radioactive wasteland with many ruinous cities (suggesting a great civilization once lived there). The identity of the fifth and final Cylon model has now been revealed to be Ellen Tigh, Colonel Saul Tigh's "deceased" wife.

Gaius Baltar's character and outlook change dramatically throughout the series, although many things about him remain constant. Baltar is a habitual womanizer and rarely turns down an opportunity to seduce someone. He is narcissistic and has a well-developed acting talent, which he uses to spin yarns on virtually any subject when he feels the need to, and occasionally (seemingly) just for practice. Almost without exception, his attempts at manipulation are accepted at face value due to his educational background, intelligence, and considerable personal charisma. However, he is sometimes exceptionally compassionate towards others and altruistic, willing to sacrifice for the good of others (especially towards the end of the series). In the final season of the series, Baltar expresses regret for having been a "profoundly selfish man" and declares that his work as a spiritual leader is his "last chance at redemption".

When the series began, Baltar was either an atheist or an agnostic, but begins to consider the existence of God to be a possibility due to the events in the first season episode "The Hand of God". Although he appears less certain about the existence of God in the fourth season episode "He That Believeth in Me", he still prays to God to take his life in the place of a sick child. Later, the child is suddenly healed. This, as well as his miraculous escape from sudden death when Internal Six asks if his prayer was sincere, and her insistence that he spread monotheistic beliefs, turn him into a monotheist. His statements in the episode "Escape Velocity" suggest that his monotheistic beliefs are more specifically panentheism.